[Bioperl-l] searchIO bug?

Jason Stajich jason.stajich at duke.edu
Thu Feb 16 09:00:01 EST 2006


i think it would be more helpful if you posted the actual report  
rather than the protein since this may be dependent on the version of  
blast you are using.

if you used
split(/\s+/, $header)
  it wouldn't matter how many spaces.

On Feb 16, 2006, at 4:24 AM, Anders Stegmann wrote:

> Hi!
>
>
> I am blasting a protein seq against an identical protein.
> I am trying to parse the protein header by using the query_description
> method in the SearchIO module.
> After using the query_description method I use split / /      in order
> to easily access the different header components.
> Here I discover that the query_description method is somehow  
> introducing
> a space between number 5 comma and the following chromosome position
> number
> in the exon chromosome position list!?
> This truncates the list of exon chromosome positions from 7 to 4,  
> later
> yielding a wrong number of the introns counted.
>
> Is this a bug?
>
> Attached is:
>
> testblast1.pl: the blastprogram to run.
>
> Q0045 the seq that is used as both query and database seq.
> (Q0045 has to be formated in order to be used as a database:  
> formatdb -i
> Q0045 -p T -o F)
>
>
> Regards Anders.
>
> <blastp5.pl>
> <Q0045>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/




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